chr2-164683151-T-C

Variant names:

• chr2-164683151-T-C
• rs6717858
• NM_001365672.2:c.*2795A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001278458.2(COBLL1):​c.*2795A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,596 control chromosomes in the GnomAD database, including 18,600 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.46 (18599 hom., cov: 30)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: COBLL1 NM_001278458.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 45 publications found

Genes affected

COBLL1 (HGNC:23571): (cordon-bleu WH2 repeat protein like 1) Enables cadherin binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001278458.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COBLL1	NM_001365672.2	MANE Select	c.*2795A>G		3_prime_UTR	Exon 14 of 14	NP_001352601.1
	COBLL1	NM_001278458.2		c.*2795A>G		3_prime_UTR	Exon 17 of 17	NP_001265387.1
	COBLL1	NM_001278460.2		c.*2795A>G		3_prime_UTR	Exon 14 of 14	NP_001265389.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COBLL1	ENST00000652658.2	MANE Select	c.*2795A>G		3_prime_UTR	Exon 14 of 14	ENSP00000498242.1
	COBLL1	ENST00000375458.6	TSL:1	c.*2795A>G		3_prime_UTR	Exon 13 of 13	ENSP00000364607.2
	COBLL1	ENST00000495084.1	TSL:3	n.126+9070A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70077 AN: 151468 Hom.: 18548 Cov.: 30

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.0900

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.418

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 2 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.463 AC: 70171 AN: 151588 Hom.: 18599 Cov.: 30 AF XY: 0.453 AC XY: 33583 AN XY: 74108

African (AFR) AF: 0.729 AC: 30072 AN: 41276

American (AMR) AF: 0.310 AC: 4713 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1244 AN: 3472

East Asian (EAS) AF: 0.0902 AC: 466 AN: 5164

South Asian (SAS) AF: 0.236 AC: 1133 AN: 4800

European-Finnish (FIN) AF: 0.350 AC: 3677 AN: 10502

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27482 AN: 67870

Other (OTH) AF: 0.415 AC: 872 AN: 2100

Alfa AF: 0.424 Hom.: 27697

Bravo AF: 0.474

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.56
PhyloP100		-0.68
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6717858; hg19: chr2-165539661;